|
| Status |
Public on Jun 15, 2014 |
| Title |
bLHF_4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Whole Large Healthy follicle
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Whole follicle
developmental stage: LargeHealthy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from whole follicles devoid of follicular fluid was extracted using miRNeasy mini kit (Qiagen) according to manufacturer’s instructions (Qiagen, UK) and analysed using the Nano Drop and Agilent Bioanalyzer 2100 (Agilent Technologies).
|
| Label |
Hy3
|
| Label protocol |
Six-hundred ng of total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| Channel 2 |
| Source name |
Pooled follicle sample (equal RNA amount from each sample)
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Whole follicle
developmental stage: Small+Large Healthy+Large Atretic
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from whole follicles devoid of follicular fluid was extracted using miRNeasy mini kit (Qiagen) according to manufacturer’s instructions (Qiagen, UK) and analysed using the Nano Drop and Agilent Bioanalyzer 2100 (Agilent Technologies).
|
| Label |
Hy5
|
| Label protocol |
Six-hundred ng of total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| |
| Hybridization protocol |
The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6th gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 16.0.
|
| Scan protocol |
The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).
|
| Description |
ch1:Hy3 array = 1_Exiqon_14326006_S01.txt
ch2:Hy5 array = 0_Exiqon_14326006_S01.txt
ch1 = Test
ch2 = Reference
|
| Data processing |
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
Values in processed data table ("Log2_FoldChanges_Test_v_Reference.txt") represent lowess normalized log2 ratio (test/reference)
|
| |
|
| Submission date |
Feb 05, 2014 |
| Last update date |
Sep 26, 2016 |
| Contact name |
Xavier Donadeu |
| E-mail(s) |
xavier.donadeu@roslin.ed.ac.uk
|
| Organization name |
Roslin Institute, University of Edinburgh
|
| Street address |
Easter Bush
|
| City |
Midlothian |
| ZIP/Postal code |
EH25 9RG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11434 |
| Series (2) |
| GSE54692 |
Expression profiling of microRNAs in Bovine ovarian follicular development |
| GSE87347 |
Expression profiling of microRNAs in Bovine ovarian follicular development; comparative analyses between LHF and CL groups |
|
